Access microbiology最新文献

Practical laboratory training is a key component of biosciences education, essential for developing critical skills and bridging the gap between theory and practice. The 'Bioskills at home kit', originally developed during the COVID-19 pandemic, was created to support first-year students in developing core laboratory skills at a time when access to in-person sessions was limited. Each kit contained equipment and guided activities focused on pipetting, microscopy, experimental design and microbial growth curve analysis. This study aimed to assess the educational impact of this kit using a mixed-methods approach. Data were collected across three student cohorts (2020/21, 2021/22 and 2024/25) using surveys and a focus group and analysed using appropriate statistical analyses and reflexive thematic analysis, respectively. The study evaluated the impact of the Bioskills at home kit on student learning across the cognitive, affective and psychomotor domains. Aspects of student experience, including perceived benefits, barriers to engagement and suggestions for improvement, were investigated, and student attainment from a compulsory laboratory assessment spanning seven academic years (2018/19-2024/25) was analysed. Results show that students experienced improved understanding of theoretical concepts, confidence, enjoyment and enhanced technical skills. Student attainment in practical assessment was also improved. Embedding the delivery of the kit in a more structured way within the personal tutorial system in subsequent years improved student engagement which was a challenge during the first year of intervention. Here, we demonstrate the successful implementation of the Bioskills at home kit which offers a scalable and inclusive model for flexible laboratory teaching.

The circular polymerase extension reaction (CPER) has emerged as a high-fidelity, versatile and rapid tool for generating infectious cDNA clones of positive-sense, single-stranded RNA viruses. Here, we implemented this strategy to generate infectious cDNA clones of two closely related members of the family Arteriviridae: equine arteritis virus KY84 strain (EAV KY84) and porcine reproductive and respiratory syndrome virus VR2332 strain (PRRSV VR2332). Overlapping cDNA fragments spanning the entire viral genomes were generated and assembled with a linker sequence incorporating critical expression elements, yielding a circularized, full-length viral cDNA genome ready for direct transfection into permissive cells. Following transfection, infectious rEAV KY84 and rPRRSV VR2332 strains were recovered and characterized. Similarly, we generated reporter viruses by inserting the mCherry gene downstream of the nsp1/nsp2 cleavage junction in EAV KY84 ORF1a and the GFP gene downstream of ORF1b of PRRSV VR2332. All CPER-generated viruses showed high identity to their parental strains by next-generation sequencing. Growth kinetics of CPER-generated non-reporter and rEAV KY84-RFP mCherry viruses were comparable to their parental strains; however, the reporter rPRRSV VR2332-GFP showed a significant reduction in viral titres despite its stability for at least 15 passages. In contrast, mCherry expression from rEAV KY84-mCherry was negligible at passage 15 and associated with the deletion of the reporter gene. Taken together, the CPER-based method can be used as a rapid tool to generate infectious cDNA clones of arteriviruses, allowing the easy generation of mutants or reporter viruses that can facilitate the investigation of viral gene functions and their interactions with the host.

Microbiology education relies heavily on visual interpretation of microbe cultures, microscopy and assays, which can create barriers for blind and visually impaired learners. Inclusive teaching requires multimodal tactile approaches that make microbiology accessible to all students. This work presents two open-source browser-based web applications (the Agar Plate STL Generator and Microscope Slide to STL) designed to convert standard microbiological images into 3D-printable tactile models. Both tools use heightmap-based image processing to translate visual data into topographic 3D surfaces. Users can upload digital images of agar plates or microscope slides (e.g. in jpg format), adjust relief depth through an interactive interface and generate printable STL files without prior experience in computer-aided design or 3D printing. The resulting tactile models replicate spatial and morphological features of microbial growth and microscopy, enabling learners to 'see through touch'. These tools enable independent participation by visually impaired students and promote multi-sensory engagement for all learners. Both applications and their source code are freely available under a Creative Commons Attribution-NonCommercial 4.0 licence via GitHub and Zenodo. Open-source tactile microbiology tools provide a scalable, inclusive means to bridge the accessibility gap in STEM education. By converting visual laboratory outputs into tangible models, these resources support universal design for learning and foster equitable participation in microbiology.

In October 2024, a putative novel species, belonging to the genus Rossellomorea, designated as strain H39_3, was isolated using Luria-Bertani medium from surface water representing station H39, located on the Hindon River, in close proximity to Gautam Buddha Nagar in Uttar Pradesh, India. The 16S rRNA sequence of this isolate showed 100% identity to Rossellomorea marisflavi from the International Nucleotide Sequence Database Collaboration (INSDC) DNA databases (GenBank/DDBJ/ENA). Whole-genome sequencing was undertaken using long-read sequencing with Oxford Nanopore Technologies (ONT) chemistry on the MinION platform, followed by genome annotation against the NCBI Reference Sequence Database (RefSeq) and Genome Taxonomy Database (GTDB) databases. The genome is ~4.46 Mb in size, with a G+C content of 48.64 mol%. The low average nucleotide identity (92.23%) and digital DNA-DNA hybridization (46.1%) values showed affiliation with the reference strain R. marisflavi, indicating the isolate as a potential novel species. Functional analysis of the draft genome of this isolate revealed an array of genes, including the presence of arsC (arsenate reductase), the assimilatory nitrate reduction pathway and the ability to degrade polysaccharides. The presence of nitrogen metabolizing genes such as nirB (nitrite reductase subunit B), along with the ability to break down complex forms of carbon, offers the potential of this strain for application in bioremediation of contaminated river ecosystems.

Fish nocardiosis, caused by Nocardia seriolae, poses a persistent threat to the aquaculture industry. Yet, the genomic determinants underlying strain-level diversity and adaptation remain poorly understood due to the high nucleotide conservation of this species. The objective of this study was to characterize genome-level variation among all publicly available complete genomes using integrative comparative genomics approaches that extend beyond nucleotide identity metrics. Nine complete genomes were analysed using average nucleotide identity, whole-genome structural rearrangement analysis, single-copy phylogenomics, genomic island prediction, pangenome reconstruction, functional annotation and antimicrobial resistance and virulence profiling. Although average nucleotide identity values confirmed extreme nucleotide conservation across all strains, extensive strain-specific structural rearrangements, including inversions, translocations and duplications, were detected. Phylogenomic reconstruction resolved geographically associated lineages despite minimal nucleotide divergence. Pangenome analyses supported an open pangenome dominated by a large, conserved core genome with limited but persistent accessory gene content and core biased gene duplication. Functional profiling revealed enrichment of transcriptional and metabolic processes, while resistance and virulence analyses identified only conserved intrinsic determinants shared across all strains. These findings demonstrate that genome architecture and pangenome dynamics provide critical resolution for understanding N. seriolae diversification. The study highlights the importance of integrating structural genomics and phylogenomics for strain tracking and surveillance in aquaculture systems.

We report the isolation and draft genome sequence of an Acinetobacter albensis strain C1-4G isolated from untreated wastewater from the Liverpool School of Tropical Medicine in Liverpool, UK. The 3.0 Mb genome contained several genes encoding alkane and aromatic hydrocarbon degrading enzymes, a qacJ antimicrobial resistance gene and several mobile genetic elements including a putative transposon, Tn7860, containing arsenic resistance genes. In addition, analysis of the biosynthetic gene clusters suggested the presence of genes that could enable the biosynthesis of baumannoferrin, a cyanobactin-type natural product, as well as a novel beta-lactone natural product.

Surface-sterilized Oryza sativa AT362 straw was screened for endophytic ligninolytic and cellulolytic bacteria using colour unit reduction and Congo Red decolorization assays. Ligninolytic Klebsiella variicola AKL1104 and cellulolytic Enterobacter chuandaensis AKC1108, biocompatible, were inoculated at a 1 : 1 ratio and incubated in 1% (w/v) rice straw broth at 37 °C for 7 days. Topological changes due to degradation were conducted using scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) for 9 days. During t=9 d, SEM shows vascular tissue perforation with tunnels, indicating K. variicola mediated-delignification, allowing E. chuandaensis to sequentially degrade cellulose. XRD revealed a cellulose crystallinity decline from 30.08% on t=0 d to 11.76% on t=9 d. Electron microscopy and crystallite size calculations in t=6 d (6.81 nm) and t=9 d (90.16 nm) indicate self-assembly of cellulose fibrils. FTIR and XPS analysis indicated crystalline cellulose transformation to amorphous cellulose as the lateral order index dropped from 0.776±0.006 to 0.503±0.007, while surface lignin coverage was reduced from 5.01 to 2.20%, respectively.

This article presents Sequenoscope: a bioinformatics pipeline for analysing Oxford Nanopore Technologies (ONT) adaptive sampling sequencing data. Sequenoscope features three main modules: filter_ONT for filtering raw reads and creating a FASTQ file with a subset of reads for further analyses, analyze for generating sequencing and read mapping statistics against the provided reference taxon sequences and plot for interactive data summarization, comparison, and visualization between two datasets/test conditions. Here, we demonstrate the ability of the pipeline to analyse ONT adaptive sampling sequence data and provide examples of the outputs users can expect using data we generated. Adaptive sampling was performed on two ZymoBIOMICS Microbial Community DNA Standards, log-distributed (Cat# D6311) and even-distributed (Cat# D6306) formulations, with targeted depletions of Listeria monocytogenes. By comparing the test and control experimental data in FASTQ files from the sequencing runs, Sequenoscope showed that depletion of L. monocytogenes was successful by providing users with parameters to compare such as taxon coverage, read length and types of pore-level decisions made during sequencing. Although Sequenoscope was designed for ONT adaptive sampling data analysis, it supports short-read data from other sequencing platforms such as Illumina, allowing for the direct comparison of any two experimental conditions or cross-platform benchmarking.

Levanderina fissa, a globally distributed mixotrophic dinoflagellate, is known for its ability to photosynthesize and phagocytize micro-organisms. This study aims to approximate the phylogenetic position and explore the morphological variability of L. fissa in Acapulco Bay, Mexico, while providing observations on its diatom feeding behaviour. Phylogenetic analysis based on 28S and 18S ribosomal DNA sequences suggests the existence of a monophyletic group within the Gymnodiniales, though with low phylogenetic resolution, indicating potential cryptic species within the genus. Morphological analysis reveals variability that may be influenced by regional environmental factors. Observations on diatom ingestion provide further, albeit limited, insights into the mixotrophic behaviour of L. fissa. These findings emphasize the need for further research to better understand the species' ecological role and phylogenetic position, particularly concerning its feeding strategies in tropical ecosystems.

Background. Antibiotic misuse, influenced by urbanization and limited healthcare access, has accelerated antibiotic resistance, impacting global health. Surveillance in Sri Lanka's National Strategic Plan for Combating Antimicrobial Resistance (2017-2022) shows significant multidrug resistance in hospitals, with 12.7% of the health budget (3.3 billion) spent on antimicrobials. This resistance complicates treatment and increases patient management costs, particularly in the Western Province, a focal area for analysing antibiotic misuse. Objectives. To assess public awareness of antibiotic misuse and antimicrobial resistance in the Western Province of Sri Lanka. Methodology. A cross-sectional study was conducted on 200 adults in the Western Province from 23 December 2023 to 16 January 2024, using in-person interviews and a Google form questionnaire. Descriptive statistics were applied to analyse the data, and a binary logistic regression analysis was conducted to identify predictors of antimicrobial resistance (AMR) knowledge among participants. The model included sociodemographic, behavioural and awareness-related variables, with statistical significance set at P<0.05. Results. Of the respondents, 83% knew antibiotics combat bacterial infections, while 71.5% adhered to completing antibiotic courses. However, 28.5% opposed doing so, with 65.5% stopping antibiotics once they felt better. Regarding antimicrobial resistance, 60.5% recognized the term, and 61% acknowledged that unnecessary antibiotic use could increase bacterial resistance. Participants from the Kalutara District had nearly nine times more good AMR knowledge (AOR=9.10, P=0.005), while those earning LKR 20,000-75,000 had almost 11 times more good knowledge (AOR=11.10, P=0.033) and those who followed the advice of a health professional had even more knowledge (AOR=851.08, P=0.016). Poor knowledge was observed from the rural population (AOR=0.15, P=0.006) and those who had ever been infected (AOR=0.21, P=0.023). Good knowledge was also present among those who had been divorced or widowed (AOR=12.21, P=0.029), had used antibiotics privately and without prescriptions (AOR=4.67, P=0.027) or who had heard of AMR but could not remember the source (AOR=51.60, P<0.001). Conclusion. Most participants understood antibiotics' role, though gaps in correct use and awareness of misuse consequences persisted. While there was a positive attitude towards antimicrobial resistance, further educational efforts are essential to address knowledge gaps, as recent studies show high resistance levels and limited progress in awareness.